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mtDNA haplogroups vs hypervariable region

Guy Hoelzer hoelzer at unr.edu
Mon Nov 6 12:21:51 EST 2000


In article <8tus6f$i9$1 at mercury.hgmp.mrc.ac.uk>, APTurner at aol.com wrote:

> > If someone has used the term "haplogroups" to mean the result of RFLP
> > analysis, I think it is a shame.  To me this term would mean something
> > like a clade of haplotypes...
> 
> I picked up the term from the MITOMAP site
> http://www.gen.emory.edu/cgi-bin/MITOMAP/bin/tbl5gen.pl

I took a quick look at that web site, and I think the confusion is yours,
not theirs.  I saw nothing that suggested haplogroups could only be
inferred from RFLP data as opposed to d-loop sequences.  They only mention
that most of the haplogroups they refer to were inferred from RFLP data. 
They could just as well have been inferred from sequence data.

> My question still remains -- is there a way to infer haplogroup from
> polymorphisms in the hypervariable region?

Sure.  This is the most common way it is done in molecular systematics.

> They seem to be two
> different approaches but shouldn't a given mitotype correspond with a
> specific haplogroup?

The web page you listed does not use the term mitotype anywhere.  This
sounds to me like it is synonymous with haplotype.  In that case, a group
is composed of a set of related types.

As far as I can see, there are not two different things going on here. 
The lab procedures are different for determining sequences vs. RFLP
patterns, but they both provide markers of DNA variation.  The analyses
lead to the same points.  RFLP data is virtually a way of identifying
sequence variants at a coarse level.

> I'm curious about the way Oxford Ancestors
> http://www.oxfordancestors.com generates their charts, with "clans"
> being named for the letter of the haplotype and the HVR-1 sequence
> reported below the chart.

I'll bet they use hypervariable region DNA sequences, but they could use
mtDNA RFLP data the same way.  The charts are generated using a
phylogenetics computer program - probably one of the commonly available
ones.  Phylogenetic methods estimate hierarchical relationships among the
haplotypes.

-- 
Guy Hoelzer
Department of Biology
University of Nevada Reno
Reno, NV  89557








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